version 2023.11.27_11.25.57 adds per-patient analysis version
2024.02.16_15.52.13 adds a table to add to appendix tables
underscore_to_space <- function(x) str_replace_all(x, "_", " ")
underscore_to_space_initial_cap <- function(x) str_replace_all(x, "_", " ") %>% str_to_sentence()
outliers <- read_tsv("../input_data/druggable_outliers_from_treehouse_and_other_cohorts_2023_11_09-13_46_32_2023.tsv") %>%
mutate(high_level_cohort = ifelse(str_detect(comparison_cohort, "Treehouse"),
"Treehouse",
comparison_cohort))
## Rows: 287 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (4): Sample_ID, comparison_cohort, gene, donor_ID
## lgl (1): pathway_support
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
n_distinct(outliers$Sample_ID)
## [1] 34
n_distinct(outliers$donor_ID)
## [1] 32
Define cohort codes
cohort_codes <- tibble(
cohort_name =
c("PEDAYA", "TCGA", "TH03_TH34", "Treehouse_pc", "Treehouse_pd"),
cohort_code =
c("P", "T", "S", "C", "D"))
Tile plot of all outliers
ggplot(outliers) +
geom_tile(aes(x=comparison_cohort,
y=gene,
fill = comparison_cohort)) +
facet_wrap(~Sample_ID,
nrow = 1) +
theme(#axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
axis.text.x = element_blank(),
strip.text.x = element_text(angle = 90),
) +
xlab("") +
scale_fill_bright()

Heatmap shows number of cohorts in which outlier were detected
I can make this look better if we decide to use it, but it’s
non-trivial
outliers_heatmap_data <- outliers %>%
group_by(Sample_ID, gene) %>%
summarize(n_outliers = n())
## `summarise()` has grouped output by 'Sample_ID'. You can override using the
## `.groups` argument.
ggplot(outliers_heatmap_data) +
geom_tile(aes(x=Sample_ID,
y=gene,
fill = n_outliers),
color = "black") +
#theme_bw() +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

library(ggVennDiagram)
raw_outliers_for_venn <- outliers %>%
mutate(sample_gene = paste(Sample_ID, gene, sep = "_")) %>%
arrange(comparison_cohort) %>%
select(sample_gene, comparison_cohort) %>%
group_split(comparison_cohort)
list_of_outliers_for_venn <- lapply(raw_outliers_for_venn, function(x) x %>% pull(sample_gene))
names(list_of_outliers_for_venn) <- unique(outliers$comparison_cohort) %>% sort
ggVennDiagram(list_of_outliers_for_venn,
show_intersect = TRUE)
## Warning in geom_text(aes_string(label = "count", text = "text"), x =
## label_coord[, : Ignoring unknown aesthetics: text
ggVennDiagram(list_of_outliers_for_venn) +
scale_fill_distiller(palette = "Reds", direction = 1)

export list of genes found only by TCGA
# outliers %>%
# group_by(Sample_ID, gene) %>%
# filter(length(comparison_cohort) == 1,
# "TCGA" %in% comparison_cohort) %>%
# ungroup %>%
# select(gene) %>% write_tsv("../gather_input_data/genes found only by TCGA in at least one sample.txt")
Annotate with combined full low level cohort names
collapse_fun <- function(x){ paste(x,collapse = ", ") }
all_outliers_combined_wide <- outliers %>%
select(-pathway_support, -donor_ID, -high_level_cohort) %>%
pivot_wider(names_from = Sample_ID,
values_from = comparison_cohort,
values_fn = collapse_fun)
n_distinct(outliers$Sample_ID)
## [1] 34
n_distinct(outliers$gene)
## [1] 56
all_outliers_combined_long <- all_outliers_combined_wide %>%
pivot_longer(-gene,
names_to = "Sample_ID",
values_to = "comparison_cohorts") %>%
na.omit()
How many outliers are present in each combination of cohorts?
tabyl(all_outliers_combined_long,
comparison_cohorts) %>%
arrange(desc(n)) %>%
adorn_pct_formatting() %>%
adorn_totals() %>%
kbl() %>%
kable_styling(full_width = F)
|
comparison_cohorts
|
n
|
percent
|
|
TCGA, Treehouse_pc
|
27
|
20.8%
|
|
TCGA
|
21
|
16.2%
|
|
Treehouse_pd
|
13
|
10.0%
|
|
TCGA, TH03_TH34, Treehouse_pc
|
12
|
9.2%
|
|
TH03_TH34
|
11
|
8.5%
|
|
PEDAYA, TCGA, TH03_TH34, Treehouse_pc
|
9
|
6.9%
|
|
TCGA, TH03_TH34, Treehouse_pc, Treehouse_pd
|
8
|
6.2%
|
|
PEDAYA, TCGA, TH03_TH34, Treehouse_pc, Treehouse_pd
|
7
|
5.4%
|
|
PEDAYA
|
5
|
3.8%
|
|
TCGA, Treehouse_pc, Treehouse_pd
|
4
|
3.1%
|
|
TCGA, TH03_TH34
|
3
|
2.3%
|
|
TCGA, Treehouse_pd
|
3
|
2.3%
|
|
PEDAYA, TCGA, Treehouse_pc, Treehouse_pd
|
2
|
1.5%
|
|
PEDAYA, TCGA, TH03_TH34
|
1
|
0.8%
|
|
PEDAYA, TCGA, Treehouse_pc
|
1
|
0.8%
|
|
PEDAYA, Treehouse_pc
|
1
|
0.8%
|
|
TH03_TH34, Treehouse_pc
|
1
|
0.8%
|
|
TH03_TH34, Treehouse_pd
|
1
|
0.8%
|
|
Total
|
130
|
|
Tile plot of combination of outliers
ggplot(all_outliers_combined_long) +
geom_tile(aes(x=Sample_ID,
y=gene,
fill = comparison_cohorts)) +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

n_distinct(all_outliers_combined_long$Sample_ID)
## [1] 34
Annotate with combined full high level cohort names
high_level_all_outliers_combined_wide <- outliers %>%
select(-pathway_support, -donor_ID, -comparison_cohort) %>%
distinct() %>%
pivot_wider(names_from = Sample_ID,
values_from = high_level_cohort,
values_fn = collapse_fun)
n_distinct(outliers$Sample_ID)
## [1] 34
n_distinct(outliers$gene)
## [1] 56
high_level_all_outliers_combined_long <- high_level_all_outliers_combined_wide %>%
pivot_longer(-gene,
names_to = "Sample_ID",
values_to = "comparison_cohorts") %>%
na.omit()
How many outliers are present in each high level combination of
cohorts?
tabyl(high_level_all_outliers_combined_long,
comparison_cohorts) %>%
arrange(desc(n)) %>%
adorn_pct_formatting() %>%
adorn_totals() %>%
kbl() %>%
kable_styling(full_width = F)
|
comparison_cohorts
|
n
|
percent
|
|
TCGA, Treehouse
|
34
|
26.2%
|
|
TCGA
|
21
|
16.2%
|
|
TCGA, TH03_TH34, Treehouse
|
20
|
15.4%
|
|
PEDAYA, TCGA, TH03_TH34, Treehouse
|
16
|
12.3%
|
|
Treehouse
|
13
|
10.0%
|
|
TH03_TH34
|
11
|
8.5%
|
|
PEDAYA
|
5
|
3.8%
|
|
PEDAYA, TCGA, Treehouse
|
3
|
2.3%
|
|
TCGA, TH03_TH34
|
3
|
2.3%
|
|
TH03_TH34, Treehouse
|
2
|
1.5%
|
|
PEDAYA, TCGA, TH03_TH34
|
1
|
0.8%
|
|
PEDAYA, Treehouse
|
1
|
0.8%
|
|
Total
|
130
|
|
Annotate with minimal combined cohort abbreviations
collapse_fun_no_coma <- function(x){ paste(x,collapse = "") }
# backslashes prevent asterisks from being interpreted as italics in the kbl table
all_outliers_min_abbrev_combined_wide <- outliers %>%
left_join(cohort_codes,
by=c("comparison_cohort"="cohort_name")) %>%
mutate(cohort_code_pathway = ifelse(pathway_support,
paste0(cohort_code, "\\*"),
cohort_code)) %>%
select(-pathway_support, -donor_ID,
-comparison_cohort,
-cohort_code) %>%
pivot_wider(names_from = Sample_ID,
values_from = cohort_code_pathway,
values_fn = collapse_fun_no_coma,
values_fill = "")
all_outliers_min_abbrev_combined_wide %>%
arrange(gene) %>%
rename_all(underscore_to_space) %>%
kbl() %>%
kable_styling(full_width = F,
bootstrap_options = "bordered")
|
gene
|
high level cohort
|
TH34 1162 S01
|
TH34 1149 S02
|
TH34 1238 S01
|
TH34 1349 S01
|
TH34 1349 S02
|
TH34 1379 S01
|
TH34 1380 S01
|
TH34 1150 S02
|
TH34 1399 S01
|
TH34 1400 S01
|
TH34 1412 S01
|
TH34 1414 S01
|
TH34 1415 S01
|
TH34 1444 S01
|
TH34 1452 S01
|
TH34 2292 S01
|
TH34 2351 S01
|
TH34 2411 S01
|
TH34 2666 S01
|
TH34 1163 S01
|
TH34 1179 S01
|
TH34 1239 S01
|
TH34 1350 S01
|
TH34 1351 S01
|
TH34 1352 S01
|
TH34 1381 S01
|
TH34 1445 S02
|
TH34 1446 S01
|
TH34 1447 S01
|
TH34 1447 S02
|
TH34 1455 S01
|
TH34 1456 S02
|
TH34 2293 S01
|
TH34 2410 S01
|
|
AKT1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ALK
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ALK
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ALK
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ALK
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BCL6
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BCL6
|
Treehouse
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
TCGA
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
TH03_TH34
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
Treehouse
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND1
|
TCGA
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND1
|
TH03_TH34
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND2
|
Treehouse
|
|
|
|
|
|
D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
CCND3
|
TCGA
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
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|
|
|
|
|
|
|
|
CCNE1
|
Treehouse
|
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|
|
|
|
|
|
|
|
|
|
|
D*
|
|
|
|
|
|
|
CDK4
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P*
|
|
|
|
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|
|
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|
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|
|
|
|
|
|
|
|
CDK4
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
S*
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
CDK4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
C*
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK9
|
TCGA
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
CDK9
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
CDK9
|
Treehouse
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
CSF1R
|
Treehouse
|
D*
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
DEPTOR
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ETV1
|
TCGA
|
|
|
|
T
|
T*
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
ETV1
|
Treehouse
|
|
|
|
C*
|
C*
|
|
|
|
|
|
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|
|
FGFR1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
T*
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
FGFR1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
FGFR2
|
TCGA
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
FGFR3
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
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|
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|
|
|
|
|
|
FGFR3
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
FGFR3
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR4
|
PEDAYA
|
|
|
|
|
|
P
|
P
|
|
|
|
P*
|
P
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
T*
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
CD
|
|
|
C*
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GATA2
|
TCGA
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
GATA2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CD*
|
|
|
|
HDAC4
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC4
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CD*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC7
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D*
|
|
|
|
HMOX1
|
PEDAYA
|
P
|
|
|
|
|
|
|
|
|
|
|
|
P*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HMOX1
|
TCGA
|
T
|
|
|
|
|
T*
|
|
|
|
|
|
|
T*
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
T*
|
|
|
|
|
|
HMOX1
|
Treehouse
|
CD*
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
C*D
|
|
|
C*
|
D*
|
|
|
|
|
|
|
|
|
|
D*
|
|
|
C
|
|
|
|
|
|
HSP90B1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
HSP90B1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
HSP90B1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
|
|
|
IGF1
|
PEDAYA
|
|
P*
|
|
|
|
|
|
|
P*
|
P*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
TCGA
|
|
T*
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
TH03_TH34
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
Treehouse
|
|
C*D
|
|
|
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF2
|
TCGA
|
|
|
|
T*
|
T*
|
T*
|
T
|
|
T*
|
|
T*
|
T*
|
|
|
T*
|
|
T*
|
|
|
T
|
|
|
|
|
T*
|
T*
|
T*
|
|
T*
|
T
|
T
|
|
T*
|
T*
|
|
IGF2
|
Treehouse
|
|
|
|
C*
|
|
D*
|
C*
|
|
C*
|
|
C*
|
C
|
|
|
C*
|
|
C*
|
|
|
C
|
|
|
|
|
C*
|
|
D*
|
|
|
C
|
C
|
|
C*
|
|
|
IL6
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
P*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
JAK1
|
PEDAYA
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
JAK1
|
TCGA
|
T
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
JAK1
|
TH03_TH34
|
S
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
JAK1
|
Treehouse
|
C
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KDR
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
KDR
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KDR
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
PEDAYA
|
|
|
|
P
|
P
|
|
|
|
|
|
|
|
|
P*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
TCGA
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
TH03_TH34
|
|
|
|
S
|
S
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
Treehouse
|
|
|
|
C
|
C
|
|
|
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K2
|
TH03_TH34
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K4
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CD*
|
|
|
|
|
|
|
|
|
|
|
|
MDM2
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P*
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MDM2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MDM2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MDM2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*D*
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MS4A1
|
PEDAYA
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MS4A1
|
TCGA
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MS4A1
|
TH03_TH34
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MS4A1
|
Treehouse
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MTOR
|
TCGA
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MTOR
|
TH03_TH34
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
NOTCH3
|
TCGA
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
NOTCH3
|
TH03_TH34
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
NOTCH3
|
Treehouse
|
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
NTRK2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
S*
|
S*
|
|
|
|
|
|
|
|
|
|
|
S*
|
S*
|
S*
|
|
|
S
|
|
|
|
|
NTRK2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
NTRK3
|
TCGA
|
|
T
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
NTRK3
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
NTRK3
|
Treehouse
|
|
CD
|
|
|
|
|
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
C
|
|
|
|
|
|
|
|
PARP1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
PARP2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
T*
|
|
|
|
|
|
PARP2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
PDCD1
|
PEDAYA
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDCD1
|
TCGA
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDCD1
|
TH03_TH34
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDCD1
|
Treehouse
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDGFRA
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
PIK3CD
|
TCGA
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3CD
|
TH03_TH34
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3CD
|
Treehouse
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
PIK3R2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D*
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R5
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R5
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
PTCH1
|
TCGA
|
|
|
|
T*
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PTCH1
|
Treehouse
|
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
RAF1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
RPTOR
|
TCGA
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
RPTOR
|
TH03_TH34
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
STAT1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
STAT2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
STAT2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
STAT2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
CD
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
STAT5A
|
Treehouse
|
|
|
|
|
|
|
|
|
|
D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
TSC2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
T*
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
TSC2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
TSC2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*D*
|
C*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
VEGFA
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
T*
|
T*
|
|
|
|
|
|
|
|
|
VEGFA
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
VEGFA
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*
|
|
|
|
|
|
|
|
|
|
C*
|
D*
|
|
|
|
|
|
|
|
|
VEGFC
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
VEGFC
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
VEGFC
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
VEGFC
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
WEE1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T*
|
|
|
|
|
|
|
|
|
WEE1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
WEE1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C*D*
|
|
|
|
|
|
|
|
Annotate with combined cohort abbreviations
all_outliers_abbrev_combined_wide <- outliers %>%
left_join(cohort_codes,
by=c("comparison_cohort"="cohort_name")) %>%
select(-pathway_support, -donor_ID,
-comparison_cohort) %>%
pivot_wider(names_from = Sample_ID,
values_from = cohort_code,
values_fn = collapse_fun,
values_fill = "")
all_outliers_abbrev_combined_wide %>%
arrange(gene) %>%
rename_all(underscore_to_space) %>%
kbl() %>%
kable_styling(full_width = F,
bootstrap_options = "bordered")
|
gene
|
high level cohort
|
TH34 1162 S01
|
TH34 1149 S02
|
TH34 1238 S01
|
TH34 1349 S01
|
TH34 1349 S02
|
TH34 1379 S01
|
TH34 1380 S01
|
TH34 1150 S02
|
TH34 1399 S01
|
TH34 1400 S01
|
TH34 1412 S01
|
TH34 1414 S01
|
TH34 1415 S01
|
TH34 1444 S01
|
TH34 1452 S01
|
TH34 2292 S01
|
TH34 2351 S01
|
TH34 2411 S01
|
TH34 2666 S01
|
TH34 1163 S01
|
TH34 1179 S01
|
TH34 1239 S01
|
TH34 1350 S01
|
TH34 1351 S01
|
TH34 1352 S01
|
TH34 1381 S01
|
TH34 1445 S02
|
TH34 1446 S01
|
TH34 1447 S01
|
TH34 1447 S02
|
TH34 1455 S01
|
TH34 1456 S02
|
TH34 2293 S01
|
TH34 2410 S01
|
|
AKT1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ALK
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ALK
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ALK
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ALK
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BCL6
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BCL6
|
Treehouse
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
TCGA
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
TH03_TH34
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
Treehouse
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND1
|
TCGA
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND1
|
TH03_TH34
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND2
|
Treehouse
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
CCND3
|
TCGA
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCNE1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
CDK4
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK4
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK9
|
TCGA
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
CDK9
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
CDK9
|
Treehouse
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
CSF1R
|
Treehouse
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
DEPTOR
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ETV1
|
TCGA
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
ETV1
|
Treehouse
|
|
|
|
C
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
T
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
FGFR1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
FGFR2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
FGFR3
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR3
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
FGFR3
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR4
|
PEDAYA
|
|
|
|
|
|
P
|
P
|
|
|
|
P
|
P
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
T
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
C
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GATA2
|
TCGA
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
GATA2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
HDAC4
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC4
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC7
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
HMOX1
|
PEDAYA
|
P
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HMOX1
|
TCGA
|
T
|
|
|
|
|
T
|
|
|
|
|
|
|
T
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
HMOX1
|
Treehouse
|
C, D
|
|
|
|
|
C, D
|
|
|
|
|
|
|
C, D
|
|
|
C
|
D
|
|
|
|
|
|
|
|
|
|
D
|
|
|
C
|
|
|
|
|
|
HSP90B1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
HSP90B1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
HSP90B1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
IGF1
|
PEDAYA
|
|
P
|
|
|
|
|
|
|
P
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
TCGA
|
|
T
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
TH03_TH34
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
Treehouse
|
|
C, D
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF2
|
TCGA
|
|
|
|
T
|
T
|
T
|
T
|
|
T
|
|
T
|
T
|
|
|
T
|
|
T
|
|
|
T
|
|
|
|
|
T
|
T
|
T
|
|
T
|
T
|
T
|
|
T
|
T
|
|
IGF2
|
Treehouse
|
|
|
|
C
|
|
D
|
C
|
|
C
|
|
C
|
C
|
|
|
C
|
|
C
|
|
|
C
|
|
|
|
|
C
|
|
D
|
|
|
C
|
C
|
|
C
|
|
|
IL6
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
JAK1
|
PEDAYA
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
JAK1
|
TCGA
|
T
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
JAK1
|
TH03_TH34
|
S
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
JAK1
|
Treehouse
|
C
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KDR
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
KDR
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KDR
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
PEDAYA
|
|
|
|
P
|
P
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
TCGA
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
TH03_TH34
|
|
|
|
S
|
S
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
Treehouse
|
|
|
|
C
|
C
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K2
|
TH03_TH34
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K4
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
MDM2
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MDM2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MDM2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MDM2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MS4A1
|
PEDAYA
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MS4A1
|
TCGA
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MS4A1
|
TH03_TH34
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MS4A1
|
Treehouse
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MTOR
|
TCGA
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MTOR
|
TH03_TH34
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
NOTCH3
|
TCGA
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
NOTCH3
|
TH03_TH34
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
NOTCH3
|
Treehouse
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
NTRK2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
S
|
S
|
|
|
|
|
|
|
|
|
|
|
S
|
S
|
S
|
|
|
S
|
|
|
|
|
NTRK2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
NTRK3
|
TCGA
|
|
T
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
NTRK3
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
NTRK3
|
Treehouse
|
|
C, D
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
C
|
|
|
|
|
|
|
|
PARP1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
PARP2
|
TCGA
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
PARP2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
PDCD1
|
PEDAYA
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDCD1
|
TCGA
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDCD1
|
TH03_TH34
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDCD1
|
Treehouse
|
|
|
|
|
|
|
|
C
|
|
|
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|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDGFRA
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
PIK3CD
|
TCGA
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3CD
|
TH03_TH34
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3CD
|
Treehouse
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
PIK3R2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R5
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
PIK3R5
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
PTCH1
|
TCGA
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PTCH1
|
Treehouse
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
RAF1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
RPTOR
|
TCGA
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
RPTOR
|
TH03_TH34
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
STAT1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
STAT2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
STAT2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
STAT2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
STAT5A
|
Treehouse
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
TSC2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
TSC2
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
TSC2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
VEGFA
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
VEGFA
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
VEGFA
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
C
|
D
|
|
|
|
|
|
|
|
|
VEGFC
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
VEGFC
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
VEGFC
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
VEGFC
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
WEE1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
WEE1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
WEE1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
SUMMARY TABLE FOR OUTLIERS DETECTED BY TREEHOUSE and OTHER COHORTS
(excludes pan-disease)
treehouse_pc_outliers <- outliers %>%
filter(comparison_cohort == "Treehouse_pc") %>%
select(Sample_ID, gene) %>%
distinct()
outliers_detected_by_treehouse_pc <- left_join(treehouse_pc_outliers,
outliers %>%
filter(comparison_cohort != "Treehouse_pd"),
by = c("Sample_ID", "gene"))
n_outliers_detected_by_treehouse_pc <- treehouse_pc_outliers %>%
nrow()
n_outliers_with_pathway_support_detected_by_treehouse_pc <- outliers_detected_by_treehouse_pc %>%
filter(pathway_support) %>%
select(Sample_ID, gene) %>%
distinct %>%
nrow()
# these have pathway support in at least one cohort
treehouse_pc_totals_tibble <- tibble(high_level_cohort= " Total",
comparison_cohort = " Total",
n_outliers_detected = n_outliers_detected_by_treehouse_pc,
n_outliers_with_pathway_support = n_outliers_with_pathway_support_detected_by_treehouse_pc,
pct_outliers_with_pathway_support = 100*n_outliers_with_pathway_support_detected_by_treehouse_pc/n_outliers_detected_by_treehouse_pc)
treehouse_pc_outlier_summary <- outliers_detected_by_treehouse_pc %>%
group_by(comparison_cohort) %>%
summarize(n_outliers_detected = n(),
n_outliers_with_pathway_support = sum(pathway_support)) %>%
ungroup() %>%
mutate(pct_outliers_detected = 100*n_outliers_detected/n_outliers_detected_by_treehouse_pc,
pct_outliers_with_pathway_support_detected =
100*n_outliers_with_pathway_support/n_outliers_with_pathway_support_detected_by_treehouse_pc,
pct_outliers_with_pathway_support = 100*n_outliers_with_pathway_support/n_outliers_detected)
treehouse_pc_outlier_summary_with_totals <-
bind_rows(treehouse_pc_outlier_summary,
treehouse_pc_totals_tibble %>% select(-high_level_cohort))
treehouse_pc_outlier_summary_with_totals %>%
rename_all(underscore_to_space) %>%
kbl(digits = c(NA, 0, 0, 0, 0)) %>%
kable_styling(full_width = F)
|
comparison cohort
|
n outliers detected
|
n outliers with pathway support
|
pct outliers detected
|
pct outliers with pathway support detected
|
pct outliers with pathway support
|
|
PEDAYA
|
20
|
10
|
28
|
19
|
NA
|
|
TCGA
|
70
|
50
|
97
|
94
|
NA
|
|
TH03_TH34
|
37
|
24
|
51
|
45
|
NA
|
|
Treehouse_pc
|
72
|
47
|
100
|
89
|
NA
|
|
Total
|
72
|
53
|
NA
|
NA
|
NA
|
SUMMARY TABLE FOR OUTLIERS DETECTED BY TREEHOUSE and OTHER
COHORTS
treehouse_outliers <- outliers %>%
filter(str_detect(high_level_cohort, "Treehouse")) %>%
select(Sample_ID, gene) %>%
distinct()
outliers_detected_by_treehouse <- left_join(treehouse_outliers,
outliers,
by = c("Sample_ID", "gene"))
n_outliers_detected_by_treehouse <- treehouse_outliers %>%
nrow()
n_outliers_with_pathway_support_detected_by_treehouse <- outliers_detected_by_treehouse %>%
filter(pathway_support) %>%
select(Sample_ID, gene) %>%
distinct %>%
nrow()
# these have pathway support in at least one cohort
treehouse_totals_tibble <- tibble(high_level_cohort= " Total",
comparison_cohort = " Total",
n_outliers_detected = n_outliers_detected_by_treehouse,
n_outliers_with_pathway_support = n_outliers_with_pathway_support_detected_by_treehouse,
pct_outliers_with_pathway_support = 100*n_outliers_with_pathway_support_detected_by_treehouse/n_outliers_detected_by_treehouse)
treehouse_outlier_summary <- outliers_detected_by_treehouse %>%
group_by(comparison_cohort) %>%
summarize(n_outliers_detected = n(),
n_outliers_with_pathway_support = sum(pathway_support)) %>%
ungroup() %>%
mutate(pct_outliers_detected = 100*n_outliers_detected/n_outliers_detected_by_treehouse,
pct_outliers_with_pathway_support_detected =
100*n_outliers_with_pathway_support/n_outliers_with_pathway_support_detected_by_treehouse,
pct_outliers_with_pathway_support = 100*n_outliers_with_pathway_support/n_outliers_detected)
treehouse_outlier_summary_with_totals <-
bind_rows(treehouse_outlier_summary,
treehouse_totals_tibble %>% select(-high_level_cohort))
treehouse_outlier_summary_with_totals %>%
rename_all(underscore_to_space) %>%
kbl(digits = c(NA, 0, 0, 0, 0)) %>%
kable_styling(full_width = F)
|
comparison cohort
|
n outliers detected
|
n outliers with pathway support
|
pct outliers detected
|
pct outliers with pathway support detected
|
pct outliers with pathway support
|
|
PEDAYA
|
20
|
10
|
22
|
15
|
NA
|
|
TCGA
|
73
|
53
|
82
|
78
|
NA
|
|
TH03_TH34
|
38
|
25
|
43
|
37
|
NA
|
|
Treehouse_pc
|
72
|
47
|
81
|
69
|
NA
|
|
Treehouse_pd
|
38
|
29
|
43
|
43
|
NA
|
|
Total
|
89
|
68
|
NA
|
NA
|
NA
|
Summary table for treehouse outliers detected by high level
cohorts
high_level_treehouse_outlier_summary <- outliers_detected_by_treehouse %>%
group_by(high_level_cohort, Sample_ID, gene) %>%
summarize(pathway_support = any(pathway_support)) %>%
group_by(high_level_cohort) %>%
summarize(n_outliers_detected = n(),
n_outliers_with_pathway_support = sum(pathway_support),
pct_outliers_with_pathway_support = 100*n_outliers_with_pathway_support/n_outliers_detected,
pct_outliers_detected = 100*n_outliers_detected/n_outliers_detected_by_treehouse)
## `summarise()` has grouped output by 'high_level_cohort', 'Sample_ID'. You can
## override using the `.groups` argument.
Function for renaming cohorts
update_cohort_strings <- function(x) {
str_replace(x,
"PEDAYA",
"Pediatric") %>%
str_replace("TH03_TH34",
"Stanford")%>%
str_replace("Treehouse_pc",
"Treehouse pan-cancer")%>%
str_replace("Treehouse_pd",
"Treehouse pan-disease") %>%
str_replace_all("_([a-z12][a-z])", " \\1")
}
Combined high and low level tables for treehouse outliers
treehouse_high_low <- bind_rows(
high_level_treehouse_outlier_summary %>%
rename(comparison_cohort=high_level_cohort) %>%
mutate(index = c(6, 5, 4, 1)),
treehouse_outlier_summary %>%
filter(str_detect(comparison_cohort, "Treehouse")) %>%
mutate(index = 2:3)
# ,
# treehouse_totals_tibble %>%
# select(-high_level_cohort) %>%
# mutate(index = 7)
) %>%
arrange(index) %>%
select(-index)
treehouse_high_low_outlier_summary <- treehouse_high_low %>%
mutate(
pct_outliers_with_pathway_support_detected =
100*n_outliers_with_pathway_support/n_outliers_with_pathway_support_detected_by_treehouse,
`Druggable outliers detected` =
paste0(n_outliers_detected, "/", n_outliers_detected_by_treehouse, " (",
round(pct_outliers_detected), "%)"),
`Druggable outliers with pathway support` =
paste0(n_outliers_with_pathway_support, "/",
n_outliers_with_pathway_support_detected_by_treehouse, " (",
round(pct_outliers_with_pathway_support_detected), "%)"),
`Fraction of druggable outliers with pathway support` =
paste0(n_outliers_with_pathway_support, "/",
n_outliers_detected, " (",
round(100*n_outliers_with_pathway_support/n_outliers_detected), "%)")
) %>%
select(comparison_cohort,
`Druggable outliers detected`,
`Druggable outliers with pathway support`,
`Fraction of druggable outliers with pathway support`) %>%
bind_rows(treehouse_totals_tibble %>%
mutate(`Fraction of druggable outliers with pathway support` =
paste0(n_outliers_with_pathway_support, "/",
n_outliers_detected, " (",
round(100*n_outliers_with_pathway_support/n_outliers_detected), "%)"),
`Druggable outliers detected` = as.character(n_outliers_detected),
`Druggable outliers with pathway support` = as.character(n_outliers_with_pathway_support)
) %>%
select(comparison_cohort,
`Druggable outliers detected`,
`Druggable outliers with pathway support`,
`Fraction of druggable outliers with pathway support`)
) %>%
mutate(comparison_cohort = update_cohort_strings(comparison_cohort))
treehouse_high_low_outlier_summary %>%
rename_all(underscore_to_space_initial_cap) %>%
kbl() %>%
kable_styling(full_width = F) %>%
add_indent(c(2, 3), level_of_indent = 1)
|
Comparison cohort
|
Druggable outliers detected
|
Druggable outliers with pathway support
|
Fraction of druggable outliers with pathway support
|
|
Treehouse
|
89/89 (100%)
|
64/68 (94%)
|
64/89 (72%)
|
|
Treehouse pan-cancer
|
72/89 (81%)
|
47/68 (69%)
|
47/72 (65%)
|
|
Treehouse pan-disease
|
38/89 (43%)
|
29/68 (43%)
|
29/38 (76%)
|
|
Stanford
|
38/89 (43%)
|
25/68 (37%)
|
25/38 (66%)
|
|
TCGA
|
73/89 (82%)
|
53/68 (78%)
|
53/73 (73%)
|
|
Pediatric
|
20/89 (22%)
|
10/68 (15%)
|
10/20 (50%)
|
|
Total
|
89
|
68
|
68/89 (76%)
|
table_output_name <- paste0("../results/treehouse_outliers_detected_relative_to_different_cohorts_", format(Sys.time(), "%Y_%m_%d-%H_%M_%S_%Y"), ".tsv")
write_tsv(treehouse_high_low_outlier_summary %>%
rename_all(underscore_to_space_initial_cap), table_output_name)
this output was saved as
../results/treehouse_outliers_detected_relative_to_different_cohorts_2024_02_16-16_12_39_2024.tsv
SUMMARY TABLE FOR OUTLIERS DETECTED BY any COHORT, INCLUDES AND LOW
LEVEL COHORTS
n_outliers_detected_by_any_method <- outliers %>%
select(Sample_ID, gene) %>%
distinct %>%
nrow()
n_outliers_with_pathway_support_detected_by_any_method <- outliers %>%
filter(pathway_support) %>%
select(Sample_ID, gene) %>%
distinct %>%
nrow()
# these have pathway support in at least one cohort
totals_tibble <- tibble(high_level_cohort= " Total",
comparison_cohort = " Total",
n_outliers_detected = n_outliers_detected_by_any_method,
n_outliers_with_pathway_support = n_outliers_with_pathway_support_detected_by_any_method,
pct_outliers_with_pathway_support = 100*n_outliers_with_pathway_support_detected_by_any_method/n_outliers_detected_by_any_method)
outlier_summary <- outliers %>%
group_by(comparison_cohort) %>%
summarize(n_outliers_detected = n(),
n_outliers_with_pathway_support = sum(pathway_support)) %>%
ungroup() %>%
mutate(pct_outliers_detected = 100*n_outliers_detected/n_outliers_detected_by_any_method,
pct_outliers_with_pathway_support_detected =
100*n_outliers_with_pathway_support/n_outliers_with_pathway_support_detected_by_any_method,
pct_outliers_with_pathway_support = 100*n_outliers_with_pathway_support/n_outliers_detected)
outlier_summary_with_totals <-
bind_rows(outlier_summary,
totals_tibble %>% select(-high_level_cohort))
outlier_summary_with_totals %>%
rename_all(underscore_to_space) %>%
kbl(digits = c(NA, 0, 0, 0, 0)) %>%
kable_styling(full_width = F)
|
comparison cohort
|
n outliers detected
|
n outliers with pathway support
|
pct outliers detected
|
pct outliers with pathway support detected
|
pct outliers with pathway support
|
|
PEDAYA
|
26
|
12
|
20
|
12
|
NA
|
|
TCGA
|
98
|
74
|
75
|
73
|
NA
|
|
TH03_TH34
|
53
|
39
|
41
|
39
|
NA
|
|
Treehouse_pc
|
72
|
47
|
55
|
47
|
NA
|
|
Treehouse_pd
|
38
|
29
|
29
|
29
|
NA
|
|
Total
|
130
|
101
|
NA
|
NA
|
NA
|
Summary table for all outliers and high level cohorts
high_level_outlier_summary <- outliers %>%
group_by(high_level_cohort, Sample_ID, gene) %>%
summarize(pathway_support = any(pathway_support)) %>%
group_by(high_level_cohort) %>%
summarize(n_outliers_detected = n(),
n_outliers_with_pathway_support = sum(pathway_support),
pct_outliers_with_pathway_support = 100*n_outliers_with_pathway_support/n_outliers_detected,
pct_outliers_detected = 100*n_outliers_detected/n_outliers_detected_by_any_method)
## `summarise()` has grouped output by 'high_level_cohort', 'Sample_ID'. You can
## override using the `.groups` argument.
high_level_outlier_summary_with_totals <-
bind_rows(high_level_outlier_summary %>%
arrange(desc(high_level_cohort)),
totals_tibble %>% select(-comparison_cohort))
high_level_outlier_summary_with_totals %>%
rename_all(underscore_to_space) %>%
kbl(format.args = list(big.mark = ","), digits = c(NA, 0, 0, 0, 0)) %>%
kable_styling(full_width = F)
|
high level cohort
|
n outliers detected
|
n outliers with pathway support
|
pct outliers with pathway support
|
pct outliers detected
|
|
Treehouse
|
89
|
64
|
72
|
68
|
|
TH03_TH34
|
53
|
39
|
74
|
41
|
|
TCGA
|
98
|
74
|
76
|
75
|
|
PEDAYA
|
26
|
12
|
46
|
20
|
|
Total
|
130
|
101
|
78
|
NA
|
Combined high and low level tables
high_low <- bind_rows(
high_level_outlier_summary_with_totals %>%
rename(comparison_cohort=high_level_cohort) %>%
mutate(index = c(1, 4:7)),
outlier_summary_with_totals %>%
filter(str_detect(comparison_cohort, "Treehouse")) %>%
mutate(index = 2:3)
) %>%
arrange(index) %>%
select(-index)
high_low_outlier_summary <- high_low %>%
filter(! str_detect(comparison_cohort, "Total")) %>%
mutate(
comparison_cohort = str_replace(comparison_cohort, "_", " "),
pct_outliers_with_pathway_support_detected =
100*n_outliers_with_pathway_support/n_outliers_with_pathway_support_detected_by_any_method,
`Druggable outliers detected` =
paste0(n_outliers_detected, "/", n_outliers_detected_by_any_method, " (",
round(pct_outliers_detected), "%)"),
`Druggable outliers with pathway support` =
paste0(n_outliers_with_pathway_support, "/",
n_outliers_with_pathway_support_detected_by_any_method, " (",
round(pct_outliers_with_pathway_support_detected), "%)"),
`Fraction of druggable outliers with pathway support` =
paste0(n_outliers_with_pathway_support, "/",
n_outliers_detected, " (",
round(100*n_outliers_with_pathway_support/n_outliers_detected), "%)")
) %>%
select(comparison_cohort,
`Druggable outliers detected`,
`Druggable outliers with pathway support`,
`Fraction of druggable outliers with pathway support`) %>%
bind_rows(totals_tibble %>%
mutate(`Fraction of druggable outliers with pathway support` =
paste0(n_outliers_with_pathway_support, "/",
n_outliers_detected, " (",
round(100*n_outliers_with_pathway_support/n_outliers_detected), "%)"),
`Druggable outliers detected` = as.character(n_outliers_detected),
`Druggable outliers with pathway support` = as.character(n_outliers_with_pathway_support)
) %>%
select(comparison_cohort,
`Druggable outliers detected`,
`Druggable outliers with pathway support`,
`Fraction of druggable outliers with pathway support`)
)
high_low_outlier_summary %>%
rename_all(underscore_to_space_initial_cap) %>%
kbl() %>%
kable_styling(full_width = F) %>%
add_indent(c(2, 3), level_of_indent = 1)
|
Comparison cohort
|
Druggable outliers detected
|
Druggable outliers with pathway support
|
Fraction of druggable outliers with pathway support
|
|
Treehouse
|
89/130 (68%)
|
64/101 (63%)
|
64/89 (72%)
|
|
Treehouse pc
|
72/130 (55%)
|
47/101 (47%)
|
47/72 (65%)
|
|
Treehouse pd
|
38/130 (29%)
|
29/101 (29%)
|
29/38 (76%)
|
|
TH03 TH34
|
53/130 (41%)
|
39/101 (39%)
|
39/53 (74%)
|
|
TCGA
|
98/130 (75%)
|
74/101 (73%)
|
74/98 (76%)
|
|
PEDAYA
|
26/130 (20%)
|
12/101 (12%)
|
12/26 (46%)
|
|
Total
|
130
|
101
|
101/130 (78%)
|
Patient level summary table for all outliers
outliers %>%
group_by(donor_ID) %>%
summarize(any_PEDAYA = "PEDAYA" %in% comparison_cohort,
any_TH03_TH34 = "TH03_TH34" %in% comparison_cohort,
any_TCGA = "TCGA" %in% comparison_cohort,
any_Treehouse_pc = "Treehouse_pc" %in% comparison_cohort,
any_Treehouse_pd = "Treehouse_pd" %in% comparison_cohort,
any_Treehouse = any_Treehouse_pc | any_Treehouse_pd) %>%
pivot_longer(starts_with("any")) %>%
mutate(name = str_remove(name, "any_")) %>%
group_by(name) %>%
summarize(n_patients_with_druggable_outliers = sum(value)) %>%
kbl() %>%
kable_styling(full_width = F)
|
name
|
n_patients_with_druggable_outliers
|
|
PEDAYA
|
18
|
|
TCGA
|
31
|
|
TH03_TH34
|
22
|
|
Treehouse
|
31
|
|
Treehouse_pc
|
30
|
|
Treehouse_pd
|
18
|
Sample level summary table for all outliers
outliers %>%
group_by(Sample_ID) %>%
summarize(any_PEDAYA = "PEDAYA" %in% comparison_cohort,
any_TH03_TH34 = "TH03_TH34" %in% comparison_cohort,
any_TCGA = "TCGA" %in% comparison_cohort,
any_Treehouse_pc = "Treehouse_pc" %in% comparison_cohort,
any_Treehouse_pd = "Treehouse_pd" %in% comparison_cohort,
any_Treehouse = any_Treehouse_pc | any_Treehouse_pd) %>%
pivot_longer(starts_with("any")) %>%
mutate(name = str_remove(name, "any_")) %>%
group_by(name) %>%
summarize(n_samples_with_druggable_outliers = sum(value)) %>%
kbl() %>%
kable_styling(full_width = F)
|
name
|
n_samples_with_druggable_outliers
|
|
PEDAYA
|
19
|
|
TCGA
|
33
|
|
TH03_TH34
|
23
|
|
Treehouse
|
33
|
|
Treehouse_pc
|
32
|
|
Treehouse_pd
|
18
|
” The genes represent 56 of the 115 druggable genes we consider
(eTable)”
all_druggable_genes <- read_tsv("../input_data/treehouseDruggableGenes_2020-03_25.txt")
## Rows: 115 Columns: 2
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (2): gene, group
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
all_druggable_genes %>%
mutate( found_as_treehouse_outlier = gene %in% (outliers %>%
filter(high_level_cohort == "Treehouse") %>%
pull(gene))) %>%
tabyl(found_as_treehouse_outlier)
## found_as_treehouse_outlier n percent
## FALSE 69 0.6
## TRUE 46 0.4
REPEAT ANALYSIS USING ONLY OUTLIERS WITH PATHWAY SUPPORT
Tile plot of outliers with pathway support
ggplot(outliers %>%
filter(pathway_support)) +
geom_tile(aes(x=comparison_cohort,
y=gene,
fill = comparison_cohort)) +
facet_wrap(~Sample_ID,
nrow = 1) +
theme(#axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
axis.text.x = element_blank(),
strip.text.x = element_text(angle = 90),
) +
xlab("") +
scale_fill_bright()

Heatmap shows number of cohorts in which outlier were detected
I can make this look better if we decide to use it, but it’s
non-trivial
pathway_outliers_heatmap_data <- outliers %>%
filter(pathway_support) %>%
group_by(Sample_ID, gene) %>%
summarize(n_outliers = n())
## `summarise()` has grouped output by 'Sample_ID'. You can override using the
## `.groups` argument.
ggplot(pathway_outliers_heatmap_data) +
geom_tile(aes(x=Sample_ID,
y=gene,
fill = n_outliers),
color = "black") +
#theme_bw() +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

raw_pathway_support_outliers_for_venn <- outliers %>%
filter(pathway_support) %>%
mutate(sample_gene = paste(Sample_ID, gene, sep = "_")) %>%
arrange(comparison_cohort) %>%
select(sample_gene, comparison_cohort) %>%
group_split(comparison_cohort)
list_of_pathway_support_outliers_for_venn <- lapply(raw_pathway_support_outliers_for_venn, function(x) x %>% pull(sample_gene))
names(list_of_pathway_support_outliers_for_venn) <- outliers %>%
filter(pathway_support) %>%
arrange(comparison_cohort) %>%
select(comparison_cohort) %>%
distinct() %>%
pull(comparison_cohort)
ggVennDiagram(list_of_pathway_support_outliers_for_venn,
show_intersect = TRUE)
## Warning in geom_text(aes_string(label = "count", text = "text"), x =
## label_coord[, : Ignoring unknown aesthetics: text
ggVennDiagram(list_of_pathway_support_outliers_for_venn) +
scale_fill_distiller(palette = "Reds", direction = 1)

Annotate with combined full cohort names
outliers_with_pathway_support_combined_wide <- outliers %>%
filter(pathway_support) %>%
select(-pathway_support, -donor_ID) %>%
pivot_wider(names_from = Sample_ID,
values_from = comparison_cohort,
values_fn = collapse_fun)
outliers_with_pathway_support_combined_long <- outliers_with_pathway_support_combined_wide %>%
pivot_longer(c(-gene, -high_level_cohort),
names_to = "Sample_ID",
values_to = "comparison_cohorts") %>%
na.omit()
How many outliers with pathway support are present in each
combination of cohorts?
tabyl(outliers_with_pathway_support_combined_long,
comparison_cohorts) %>%
arrange(desc(n)) %>%
adorn_pct_formatting() %>%
adorn_totals() %>%
kbl() %>%
kable_styling(full_width = F)
|
comparison_cohorts
|
n
|
percent
|
|
TCGA
|
74
|
39.2%
|
|
TH03_TH34
|
39
|
20.6%
|
|
Treehouse_pc
|
35
|
18.5%
|
|
Treehouse_pd
|
17
|
9.0%
|
|
PEDAYA
|
12
|
6.3%
|
|
Treehouse_pc, Treehouse_pd
|
12
|
6.3%
|
|
Total
|
189
|
|
ggplot(outliers_with_pathway_support_combined_long) +
geom_tile(aes(x=Sample_ID,
y=gene,
fill = comparison_cohorts)) +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

n_distinct(outliers_with_pathway_support_combined_long$Sample_ID)
## [1] 32
Patient level summary table for outliers with pathway support
outliers %>%
filter(pathway_support) %>%
group_by(donor_ID) %>%
summarize(any_PEDAYA = "PEDAYA" %in% comparison_cohort,
any_TH03_TH34 = "TH03_TH34" %in% comparison_cohort,
any_TCGA = "TCGA" %in% comparison_cohort,
any_Treehouse_pc = "Treehouse_pc" %in% comparison_cohort,
any_Treehouse_pd = "Treehouse_pd" %in% comparison_cohort,
any_Treehouse = any_Treehouse_pc | any_Treehouse_pd) %>%
pivot_longer(starts_with("any")) %>%
mutate(name = str_remove(name, "any_")) %>%
group_by(name) %>%
summarize(n_patients_with_druggable_outliers = sum(value)) %>%
kbl() %>%
kable_styling(full_width = F)
|
name
|
n_patients_with_druggable_outliers
|
|
PEDAYA
|
8
|
|
TCGA
|
26
|
|
TH03_TH34
|
16
|
|
Treehouse
|
26
|
|
Treehouse_pc
|
22
|
|
Treehouse_pd
|
13
|
Annotate with combined cohort abbreviations
outliers_with_pathway_support_abbrev_combined_wide <- outliers %>%
filter(pathway_support) %>%
left_join(cohort_codes,
by=c("comparison_cohort"="cohort_name")) %>%
select(-pathway_support, -donor_ID,
-comparison_cohort) %>%
pivot_wider(names_from = Sample_ID,
values_from = cohort_code,
values_fn = collapse_fun,
values_fill = "")
Big table of outliers with pathway support
outliers_with_pathway_support_abbrev_combined_wide %>%
arrange(gene) %>%
rename_all(underscore_to_space) %>%
kbl() %>%
kable_styling(full_width = F,
bootstrap_options = "bordered")
|
gene
|
high level cohort
|
TH34 1149 S02
|
TH34 1238 S01
|
TH34 1399 S01
|
TH34 1400 S01
|
TH34 1412 S01
|
TH34 1415 S01
|
TH34 1444 S01
|
TH34 1452 S01
|
TH34 2292 S01
|
TH34 2411 S01
|
TH34 1179 S01
|
TH34 1239 S01
|
TH34 1349 S01
|
TH34 1349 S02
|
TH34 1350 S01
|
TH34 1352 S01
|
TH34 1379 S01
|
TH34 1380 S01
|
TH34 1381 S01
|
TH34 1150 S02
|
TH34 1414 S01
|
TH34 1445 S02
|
TH34 1447 S01
|
TH34 1447 S02
|
TH34 1455 S01
|
TH34 1456 S02
|
TH34 2293 S01
|
TH34 2351 S01
|
TH34 2410 S01
|
TH34 1446 S01
|
TH34 1162 S01
|
TH34 1351 S01
|
|
AKT1
|
TH03_TH34
|
|
|
|
|
|
|
S
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT1
|
Treehouse
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
PEDAYA
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
TCGA
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
TH03_TH34
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
AKT2
|
Treehouse
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BCL6
|
TCGA
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
TCGA
|
|
T
|
|
|
|
|
|
|
|
|
|
T
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
TH03_TH34
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
BTK
|
Treehouse
|
|
C
|
|
|
|
|
|
|
|
|
|
C
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCND3
|
TCGA
|
|
T
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CCNE1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
CDK4
|
PEDAYA
|
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK4
|
TCGA
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK4
|
Treehouse
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
CDK9
|
TCGA
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
CSF1R
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
DEPTOR
|
TH03_TH34
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ETV1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
ETV1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
C
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR1
|
TCGA
|
|
|
|
|
|
|
|
|
|
T
|
T
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR3
|
TCGA
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR3
|
TH03_TH34
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FGFR4
|
PEDAYA
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
PEDAYA
|
|
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
TCGA
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
TH03_TH34
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
FLT4
|
Treehouse
|
|
|
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GATA2
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
GATA2
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
HDAC4
|
TCGA
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC4
|
TH03_TH34
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC4
|
Treehouse
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HDAC7
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
D
|
|
|
|
|
|
|
|
HMOX1
|
PEDAYA
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HMOX1
|
TCGA
|
|
|
|
|
|
T
|
|
|
T
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
T
|
T
|
|
|
|
|
|
|
|
|
|
HMOX1
|
Treehouse
|
|
|
|
|
|
C
|
|
|
C
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
D
|
|
|
|
|
|
D
|
|
|
D
|
|
|
HSP90B1
|
TCGA
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HSP90B1
|
TH03_TH34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
HSP90B1
|
Treehouse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
PEDAYA
|
P
|
|
P
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
TCGA
|
T
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
TH03_TH34
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF1
|
Treehouse
|
C
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IGF2
|
TCGA
|
|
|
T
|
|
T
|
|
|
T
|
|
|
|
|
T
|
T
|
|
T
|
T
|
|
T
|
|
T
|
T
|
T
|
|
|
|
T
|
T
|
T
|
|
|
|
|
IGF2
|
Treehouse
|
|
|
C
|
|
C
|
|
|
C
|
|
|
|
|
C
|
|
|
C
|
D
|
C
|
|
|
|
D
|
|
|
|
|
C
|
C
|
|
|
|
|
|
IL6
|
PEDAYA
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
TCGA
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
TH03_TH34
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IL6
|
Treehouse
|
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KDR
|
TCGA
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
KDR
|
TH03_TH34
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KDR
|
Treehouse
|
|
|
|
|
C
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
PEDAYA
|
|
|
|
|
|
|
P
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
TCGA
|
|
|
|
|
|
|
T
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
TH03_TH34
|
|
|
|
|
|
|
S
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KIT
|
Treehouse
|
|
|
|
|
|
|
C, D
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
MAP2K2
|
TCGA
|
|
|
|
|
|
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PIK3R2
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PIK3R5
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PIK3R5
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C
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PTCH1
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PTCH1
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C
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RAF1
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RPTOR
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STAT5A
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VEGFA
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VEGFA
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Treehouse
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VEGFC
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PEDAYA
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VEGFC
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VEGFC
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VEGFC
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Treehouse
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C, D
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WEE1
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WEE1
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Treehouse
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C, D
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Detail table for all samples
table_output_name <- paste0("../results/detailed_treehouse_outliers_detected_relative_to_different_cohorts_", format(Sys.time(), "%Y_%m_%d-%H_%M_%S_%Y"), ".tsv")
outliers %>%
rename(outlier_gene = gene) %>%
mutate(original_comparison_cohort_name = comparison_cohort,
comparison_cohort = update_cohort_strings(original_comparison_cohort_name)) %>%
arrange(Sample_ID,
outlier_gene,
comparison_cohort) %>%
select(Dataset = Sample_ID,
`Outlier gene` = outlier_gene,
`Comparison cohort` = comparison_cohort,
`Pathway support` = pathway_support) %>%
write_tsv(table_output_name)
this output was saved as
../results/detailed_treehouse_outliers_detected_relative_to_different_cohorts_2024_02_16-16_12_43_2024.tsv
sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Monterey 12.2
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggVennDiagram_1.2.2 cowplot_1.1.1 gridExtra_2.3
## [4] kableExtra_1.3.4 khroma_1.10.0 janitor_2.1.0
## [7] forcats_0.5.2 stringr_1.5.0 dplyr_1.0.10
## [10] purrr_0.3.5 readr_2.1.3 tidyr_1.2.1
## [13] tibble_3.2.1 ggplot2_3.4.4 tidyverse_1.3.2
##
## loaded via a namespace (and not attached):
## [1] fs_1.6.3 sf_1.0-9 lubridate_1.9.0
## [4] bit64_4.0.5 RColorBrewer_1.1-3 webshot_0.5.4
## [7] httr_1.4.4 tools_4.2.1 backports_1.4.1
## [10] bslib_0.5.0 utf8_1.2.3 R6_2.5.1
## [13] KernSmooth_2.23-20 lazyeval_0.2.2 DBI_1.1.3
## [16] colorspace_2.1-0 withr_2.5.0 tidyselect_1.2.0
## [19] bit_4.0.5 compiler_4.2.1 cli_3.6.1
## [22] rvest_1.0.3 xml2_1.3.3 plotly_4.10.1
## [25] labeling_0.4.2 sass_0.4.7 scales_1.2.1
## [28] classInt_0.4-9 proxy_0.4-27 systemfonts_1.0.4
## [31] digest_0.6.33 yulab.utils_0.0.6 rmarkdown_2.23
## [34] svglite_2.1.0 pkgconfig_2.0.3 htmltools_0.5.5
## [37] dbplyr_2.2.1 fastmap_1.1.1 highr_0.10
## [40] htmlwidgets_1.6.2 rlang_1.1.1 readxl_1.4.1
## [43] rstudioapi_0.14 jquerylib_0.1.4 farver_2.1.1
## [46] generics_0.1.3 jsonlite_1.8.7 crosstalk_1.2.0
## [49] vroom_1.6.0 googlesheets4_1.0.1 magrittr_2.0.3
## [52] Rcpp_1.0.11 munsell_0.5.0 fansi_1.0.4
## [55] lifecycle_1.0.3 stringi_1.7.12 yaml_2.3.7
## [58] snakecase_0.11.0 grid_4.2.1 parallel_4.2.1
## [61] crayon_1.5.2 haven_2.5.1 hms_1.1.2
## [64] knitr_1.43 pillar_1.9.0 reprex_2.0.2
## [67] glue_1.6.2 evaluate_0.21 data.table_1.14.6
## [70] modelr_0.1.10 vctrs_0.6.3 tzdb_0.3.0
## [73] cellranger_1.1.0 gtable_0.3.3 assertthat_0.2.1
## [76] cachem_1.0.8 xfun_0.39 broom_1.0.1
## [79] e1071_1.7-13 class_7.3-20 googledrive_2.0.0
## [82] RVenn_1.1.0 viridisLite_0.4.2 gargle_1.2.1
## [85] units_0.8-1 timechange_0.1.1 ellipsis_0.3.2